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- PDB-4v10: Skelemin Association with alpha2b,beta3 Integrin: A Structural Model -

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Basic information

Entry
Database: PDB / ID: 4v10
TitleSkelemin Association with alpha2b,beta3 Integrin: A Structural Model
ComponentsMYOMESIN-1
KeywordsSTRUCTURAL PROTEIN / INTEGRIN
Function / homology
Function and homology information


extraocular skeletal muscle development / myosin filament / M band / protein kinase A signaling / sarcomere / muscle contraction / positive regulation of protein secretion / structural constituent of cytoskeleton / kinase binding / cytoskeleton ...extraocular skeletal muscle development / myosin filament / M band / protein kinase A signaling / sarcomere / muscle contraction / positive regulation of protein secretion / structural constituent of cytoskeleton / kinase binding / cytoskeleton / positive regulation of gene expression / protein homodimerization activity / identical protein binding
Similarity search - Function
Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype ...Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMUS MUSCULUS (house mouse)
MethodSOLUTION NMR / ARIA, XPLOR-NIH
AuthorsGorbatyuk, V. / Deshmukh, L. / Nguyen, K. / Vinogradova, O.
CitationJournal: Biochemistry / Year: 2014
Title: Skelemin Association with Alphaiibbeta3 Integrin: A Structural Model.
Authors: Gorbatyuk, V. / Nguyen, K. / Podolnikova, N.P. / Deshmukh, L. / Lin, X. / Ugarova, T.P. / Vinogradova, O.
History
DepositionSep 19, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2014Group: Atomic model
Revision 1.2Nov 19, 2014Group: Database references
Revision 1.3Jan 24, 2018Group: Data collection / Database references / Structure summary
Category: citation / pdbx_nmr_spectrometer / struct / Item: _citation.page_last / _struct.title
Revision 1.4Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MYOMESIN-1


Theoretical massNumber of molelcules
Total (without water)27,0931
Polymers27,0931
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1000LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein MYOMESIN-1 / / MYOMESIN FAMILY MEMBER 1 / SKELEMIN / SK45


Mass: 27092.945 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1208-1434 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Tissue: MUSCULES / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: Q62234

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HSQC
121TRIPLE-RESONANCE BACKBONE EXPERIMENTS
131TOCSY
141NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED SKELEMIN 4,5

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Sample preparation

DetailsContents: 20 MM KPI,1 MM DSS, 90% WATER/ 10% D2O
Sample conditionsIonic strength: 20 mM / pH: 6.8 / Pressure: 1.0 atm / Temperature: 298.0 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Xplor-NIHG. MARIUS CLORE , GUILLERMO BERMEJO, JOHN KUSZEWSKI, CHARLES D. SCHWIETERS, NICO TJrefinement
CcpNmr Analysis2.4structure solution
ARIA2.3structure solution
CcpNmr Analysis2.2structure solution
Xplor-NIH2.33structure solution
NMRPipe0structure solution
DANGLE1.1structure solution
RefinementMethod: ARIA, XPLOR-NIH / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 1000 / Conformers submitted total number: 20

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